In silico analysis for determining the deleterious nonsynonymous single nucleotide polymorphisms of BRCA genes

1. Easton DF, Ford D, Bishop DT. Breast and ovarian cancer incidence in BRCA1-mutation carriers. Breast Cancer Linkage Consortium. Am J Hum Genet 1995;56:265-271.

2. Hopper JL, Southey MC, Dite GS, Jolley DJ, Giles GG, McCredie MR, Easton DF,Venter DJ. Population-based estimate of the average age-specific cumulative risk of breast cancer for a defined set of protein-truncating mutations in BRCA1 and BRCA2. Cancer Epidem Biomar 1999;8:741-747.

3. Wu LC, Wang ZW, Tsan JT, Spillman MA, Phung A, Xu XL, Yang MC, Hwang LY, Bowcock AM, Baer R. Identification of a RING protein that can interact in vivo with the BRCA1 gene product. Nat Genet 1996;14:430-440.

4. Scully R, Chen J, Plug A, Xiao Y, Weaver D, Feunteun J, Ashley T, Livingston DM. Association of BRCA1 with Rad51 in mitotic and meiotic cells. Cell 1997;88:265-275.

5. Koonin EV, Altschul SF, Bork P. BRCA1 protein products... Functional motifs... Nat Genet 1996;13:266-268.

6. Bork P, Hofmann K, Bucher P, Neuwald A, Altschul S, Koonin E. A superfamily of conserved domains in DNA damage-responsive cell cycle checkpoint proteins. FASEB J 1997;11:68-76.

7. Callebaut I, Mornon JP. From BRCA1 to RAP1: a widespread BRCT module closely associated with DNA repair. FEBS Lett 1997;400:25-30.

8. Friedman LS, Ostermeyer EA, Szabo CI, Dowd P, Lynch ED, Rowell SE, King MC. Confirmation of BRCA1 by analysis of germline mutations linked to breast and ovarian cancer in ten families. Nat Genet 1994;8:399-404.

9. Gayther SA, Warren W, Mazoyer S, Russell PA, Harrington PA, Chiano M, Seal S, Hamoudi R, van Rensburg EJ, Dunning AM. Germline mutations of the BRCA1 gene in breast and ovarian cancer families provide evidence for a genotype-phenotype correlation. Nat Genet 1995;11:428-433.

10. Shen D,Vadgama JV. BRCA1 and BRCA2 gene mutation analysis: visit to the Breast Cancer Information Core (BIC). Oncol Res 1999;11: 63-69.

11. Bork P, Blomberg N, Nilges M. Internal repeats in the BRCA2 protein sequence. Nat Genet 1996;13:22-23.

12. Chen PL, Chen CF, Chen Y, Xiao J, Sharp ZD, Lee WH. The BRC repeats in BRCA2 are critical for RAD51 binding and resistance to methyl methanesulfonate treatment. Proc Natl Acad Sci USA 1998;95:5287-5292.

13. Yang H, Jeffrey PD, Miller J, Kinnucan E, Sun Y, Thomä NH, Zheng N, Chen PL, Lee WH, Pavletich NP. BRCA2 function in DNA binding and recombination from a BRCA2-DSS1-ssDNA structure.Science. 2002;297:1837-1848.

14. George DC, Chakraborty C, Haneef SA, NagaSundaram N, Chen L, Zhu H. Evolution-and structure-based computational strategy reveals the impact of deleterious missense mutations on MODY 2 (maturity-onset diabetes of the young, type 2). Theranostics. 2014;4:366-385.

15. Pires AS, Porto WF, Franco OL, Alencar SA. In silico analyses of deleterious missense SNPs of human apolipoprotein E3. Sci Rep 2017;7: 2509.

16. Plon SE, Eccles DM, Easton D, Foulkes WD, Genuardi M, Greenblatt MS, Hogervorst FB, Hoogerbrugge N, Spurdle AB, Tavtigian SV. Sequence variant classification and reporting: recommendations for improving the interpretation of cancer susceptibility genetic test results. Hum Mutat 2008;29:1282-1291.

17. Kumar P, Henikoff S, Ng PC. Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm. Nat Protoc 2009;4:1073-1081.

18 Adzhubei IA, Schmidt S, Peshkin L, Ramensky VE, Gerasimova A, Bork P, Kondrashov AS,Sunyaev SR. A method and server for predicting damaging missense mutations. Nat Methods 2010;7: 248-249.

19. Capriotti E, Calabrese R, Casadio R. Predicting the insurgence of human genetic diseases associated to single point protein mutations with support vector machines and evolutionary information. Bioinformatics 2006;22:2729-2734.

20. Shihab HA, Gough J, Cooper DN, Stenson PD, Barker GL, Edwards KJ, Day IN, Gaunt TR. Predicting the functional, molecular, and phenotypic consequences of amino acid substitutions using hidden Markov models. Hum Mutat 2013;34:57-65.

21. Mi H, Guo N, Kejariwal A,Thomas PD. PANTHER version 6: protein sequence and function evolution data with expanded representation of biological pathways. Nucleic Acids Res 2007;35(suppl 1):D247-D252.

22. Bromberg Y, Rost B. SNAP: predict effect of non-synonymous polymorphisms on function. Nucleic Acids Res 2007;35:3823-3835.

23. Calabrese R, Capriotti E, Fariselli P, Martelli PL, Casadio R. Functional annotations improve the predictive score of human disease‐related mutations in proteins. Hum Mutat 2009;30:1237-1244.

24. Tavtigian SV, Deffenbaugh AM, Yin L, Judkins T, Scholl T, Samollow PB, de Silva D, Zharkikh A, Thomas A. Comprehensive statistical study of 452 BRCA1 missense substitutions with classification of eight recurrent substitutions as neutral. J Med Genet 2006; 43:295-305.

25. Mathe E, Olivier M, Kato S, Ishioka C, Hainaut P, Tavtigian SV. Computational approaches for predicting the biological effect of p53 missense mutations: a comparison of three sequence analysis based methods. Nucleic Acids Res 2006;34:1317-1325.

26. Capriotti E, Fariselli P, Rossi I, Casadio R. A three-state prediction of single point mutations on protein stability changes. BMC Bioinformatics 2008;9 (Suppl 2):S6.

27. Landau M, Mayrose I, Rosenberg Y, Glaser F, Martz E, Pupko T, Ben-Tal N. ConSurf 2005: the projection of evolutionary conservation scores of residues on protein structures. Nucleic Acids Res 2005;33(suppl 2):W299-W302.

28. Šali A, Blundell TL. Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol 1993; 234:779-815.

29. Laskowski RA, MacArthur MW, Moss DS,Thornton JM. PROCHECK: a program to check the stereochemical quality of protein structures.J Appl Cryst 1993;26:283-291.

30. Laskowski RA, Rullmann JA, MacArthur MW, Kaptein R,Thornton JM. AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR. J Biomol NMR 1996;8:477-486.

31. Van Durme J, Delgado J, Stricher F, Serrano L, Schymkowitz J,Rousseau F. A graphical interface for the FoldX forcefield. Bioinformatics 2011;27:1711-1712.

32. Krieger E, Koraimann G,Vriend G. Increasing the precision of comparative models with YASARA NOVA-a self-parameterizing force field. Proteins 2002;47:393-402.

33. Chan PA, Duraisamy S, Miller PJ, Newell JA, McBride C, Bond JP, Raevaara T, Ollila S, Nyström M, Grimm AJ. Christodoulou J, Oetting WS, Greenblatt MS. Interpreting missense variants: comparing computational methods in human disease genes CDKN2A, MLH1, MSH2, MECP2, and tyrosinase (TYR). Hum Mutat 2007;28:683-693.

34. Williams RS, Green R, Glover JN. Crystal structure of the BRCT repeat region from the breast cancer-associated protein BRCA1. Nat Struct Biol. 2001;8:838-842.

35. Brzovic PS, Rajagopal P, Hoyt DW, King MC, Klevit RE. Structure of a BRCA1-BARD1 heterodimeric RING-RING complex. Nat Struct Biol 2001;8:833-837.

36. Tokuriki N, Stricher F, Schymkowitz J, Serrano L, Tawfik DS. The stability effects of protein mutations appear to be universally distributed. J Mol Biol 2007;369:1318-1332.

37. Stehr H, Jang SH, Duarte JM, Wierling C, Lehrach H, Lappe M, Lange BM. The structural impact of cancer-associated missense mutations in oncogenes and tumor suppressors. Mol Cancer 2011;10:54.

38. Goldgar DE, Easton DF, Deffenbaugh AM, Monteiro AN, Tavtigian SV, Couch FJ. Integrated evaluation of DNA sequence variants of unknown clinical significance: application to BRCA1 and BRCA2. Am J Hum Genet 2004;75:535-544.

39. Rowling PJ, Cook R,Itzhaki LS. Toward classification of BRCA1 missense variants using a biophysical approach. J Biol Chem 2010;285:20080-20087.

40. Mirkovic N, Marti-Renom MA, Weber BL, Sali A, Monteiro AN. Structure-based assessment of missense mutations in human BRCA1: implications for breast and ovarian cancer predisposition. Cancer Res 2004;64:3790-3797.

41. Lee MS, Green R, Marsillac SM, Coquelle N, Williams RS, Yeung T, Foo D, Hau DD, Hui B, Monteiro AN, Glover JN. Comprehensive analysis of missense variations in the BRCT domain of BRCA1 by structural and functional assays. Cancer Res 2010;70:4880-4890.

42. Yadegari F, Farahmand L, Esmaeili R, Samadi T, Majidzadeh K. Functional investigation of the BRCA1 Val1714Gly and Asp1733Gly variants by computational tools and yeast transcription activation assay. Mol Biol Res Commun 2019;8:113-118.

43. Gaiser OJ, Ball LJ, Schmieder P, Leitner D, Strauss H, Wahl M, Kühne R, Oschkinat H, Heinemann U. Solution structure, backbone dynamics, and association behavior of the C-terminal BRCT domain from the breast cancer-associated protein BRCA1. Biochemistry 2004;43:15983-15995.

44. Greenblatt M, Beaudet JG, Gump JR, Godin KS, Trombley L, Koh J, Bond JP. Detailed computational study of p53 and p16: using evolutionary sequence analysis and disease-associated mutations to predict the functional consequences of allelic variants. Oncogene 2003;22:1150-1163.

45. Rishishwar L, Varghese N, Tyagi E, Harvey SC, Jordan IK, McCarty NA. Relating the disease mutation spectrum to the evolution of the cystic fibrosis transmembrane conductance regulator (CFTR) PLoS One 2012;7:e42336.

46. Rajith B, C GP. Path to facilitate the prediction of functional amino acid substitutions in red blood cell disorders--a computational approach. PLoS One 2011;6:e24607.